Ann Clin Microbiol.  2025 Mar;28(1):2. 10.5145/ACM.2025.28.1.2.

Composition, developmental patterns, and pathological associations of the human gut mycobiome

• Lee EH
• Hong CR

• KMID: 2566598
• DOI: http://doi.org/10.5145/ACM.2025.28.1.2

Abstract

Purpose
The human gut mycobiome comprises diverse fungal species and plays a crucial role in health and disease, despite its relatively low abundance compared to bacterial populations. This review provides an overview of the mycobiome’s composition, developmental patterns, and dysbiosis in various pathological conditions. As well, the complex interactions of fungal communities within the gut microbiome are discussed. Current content: The development of the gut mycobiome follows patterns similar to those of the bacterial microbiome, with birth mode, diet, and age being key determinants. In contrast to the bacterial trends, mycobiome diversity increases during childhood and old age. Recent studies have revealed variations in the mycobiome composition across different ethnic groups. Mycobiome dysbiosis is associated with autoimmune, gastrointestinal, and cardiovascular diseases. Certain fungi, notably Candida albicans, are relatively more abundant in pathological states. Fungal metabolic activity, particularly secondary metabolite production, can significantly affect disease progression. Bacterial–fungal interactions in the gut microbiome are complex and modulated by environmental factors, such as diet and antibiotic use. Moreover, the gut mycobiome modulates therapeutic efficacy. Gut fungi enhance the bioactivity of compounds derived from natural products through biotransformation, including their anticancer and anti-inflammatory effects. This suggests the potential of the gut mycobiome to optimize the therapeutic efficacy of natural products.
Conclusion
This review highlights the relevance of the gut mycobiome as both a diagnostic biomarker and a therapeutic target. Future research should focus on elucidating the causal relationships between mycobiome alterations and disease states, and further explore bacterial–fungal interactions within the gut ecosystem.

Keyword

Biotransformation; Candida albicans; Dysbiosis; Microbial interactions; Mycobiome

Figure

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  Fig. 1. Spatial distribution of mycobiota within the human host.

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  Fig. 2. Mechanisms and consequences of bacterial–fungal interactions. Bacterial and fungal species modulate fungal growth in human hosts via diverse mechanisms. QS, quorum sensing; SCFA, short-chain fatty acid.

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